FB2024_03 , released June 25, 2024
Gene: Dmel\mir-10
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General Information
Symbol
Dmel\mir-10
Species
D. melanogaster
Name
mir-10 stem loop
Annotation Symbol
CR42977
Feature Type
miRNA_gene
FlyBase ID
FBgn0262424
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

dme-mir-10, miR-10*, mir-10S

Key Links
Genomic Location
Cytogenetic map
84A5-84A5
Sequence location
Recombination map
3-48
RefSeq locus
NT_033777 REGION:6809506..6809582
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (4 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables mRNA base-pairing translational repressor activity
inferred from direct assay
(He et al., 2022)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in miRNA-mediated post-transcriptional gene silencing
inferred from direct assay
(He et al., 2022)
involved_in negative regulation of smoothened signaling pathway
inferred from mutant phenotype
(He et al., 2022)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in miRNA-mediated post-transcriptional gene silencing
inferred from electronic annotation with Rfam:RF00104
(RNAcentral, 2018-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of RISC complex
inferred from electronic annotation with Rfam:RF00104
(RNAcentral, 2018-)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
    -
    Summaries
    Pathway (FlyBase)
    Negative Regulators of Hedgehog Signaling Pathway -
    Negative regulators of hedgehog signaling down-regulate the pathway, resulting in the repression of transcription of hh-responsive genes.
    Gene Model and Products
    Number of Transcripts
    3
    Number of Unique Polypeptides
    0

    Please see the JBrowse view of Dmel\mir-10 for information on other features

    To submit a correction to a gene model please use the Contact FlyBase form

    Protein Domains (via Pfam)
    Isoform displayed:
    Pfam protein domains
    InterPro name
    classification
    start
    end
    Protein Domains (via SMART)
    Isoform displayed:
    SMART protein domains
    InterPro name
    classification
    start
    end
    Structure
    Experimentally Determined Structures
    Crossreferences
    Comments on Gene Model

    Locations and structures of miRNA models as mapped by miRBase (FBrf0220601).

    Conserved: found throughout the Drosophila genus (FBrf0230987).

    Sequence Ontology: Class of Gene
    miRNA_gene
    (FlyBase Genome Annotators, 2010, Lagos-Quintana et al., 2001)
    nuclear_gene
    (FlyBase Genome Annotators, 2010, Lagos-Quintana et al., 2001)
    Transcript Data
    Annotated Transcripts
    Name
    FlyBase ID
    RefSeq ID
    Length (nt)
    mir-10-RA
    FBtr0304381
    NR_048338
    22
    mir-10-RB
    FBtr0304382
    NR_048337
    23
    mir-10-RM
    FBtr0304380
    NR_048336
    77
    Additional Transcript Data and Comments
    Reported size (kB)
    Comments
    External Data
    Crossreferences
    miRBase - A searchable database of published miRNA sequences and annotation.
    Sequences Consistent with the Gene Model
    Nucleotide / Polypeptide Records
    Mapped Features

    Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\mir-10 using the Feature Mapper tool.

    External Data
    Crossreferences
    Linkouts
    Expression Data
    Testis-specificity index

    The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

    NA

    Transcript Expression
    in situ
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    embryonic stage 4 -- 5
    organism | 50-80% egg length
    (Lemons et al., 2012)
    organism | pair rule expression pattern
    (Lemons et al., 2012)
    embryonic stage 5
    organism | 50-80% egg length
    (Aboobaker et al., 2005)
    embryonic stage 5 -- 6
    organism | striped
    (Aboobaker et al., 2005)
    embryonic stage 9 -- 11
    anal pad primordium
    (Lemons et al., 2012)
    embryonic primordium of adult hindgut precursor
    (Lemons et al., 2012)
    ventral nerve cord primordium
    (Lemons et al., 2012)
    embryonic stage 11
    larval ventral nerve cord
    (Aboobaker et al., 2005)
    posterior midgut primordium
    (Aboobaker et al., 2005)
    embryonic stage 11 -- 14
    embryonic hindgut
    (Aboobaker et al., 2005)
    embryonic stage 14
    anal pad primordium
    (Aboobaker et al., 2005)
    embryonic stage 14 -- 16
    anal pad primordium
    (Lemons et al., 2012)
    endoderm of embryonic/larval hindgut
    (Lemons et al., 2012)
    endoderm of embryonic/larval midgut
    (Lemons et al., 2012)
    larval ventral nerve cord
    (Lemons et al., 2012)
    northern blot
    Stage
    Tissue/Position (including subcellular localization)
    Reference
    embryonic stage 1 -- 16
    organism
    (Lemons et al., 2012)
    Additional Descriptive Data

    In-situ hybridization using locked nucleic acids showed expression of mir-10-5p and mir-10-3p in the same pattern as pri-mir-10. Northern blots detecting mir-10-5p and mir-10-3p showed that while both increase in expression throughtout embryogenesis, mir-10-3p is more abundant than mir-10-5p. mir-10 is not highly expressed in cells with high levels of Scr or Abd-B, two of its predicted targets.

    (Lemons et al., 2012)
    Marker for
     
    Subcellular Localization
    CV Term
    Polypeptide Expression
    Additional Descriptive Data
    Marker for
     
    Subcellular Localization
    CV Term
    Evidence
    References
    Expression Deduced from Reporters
    High-Throughput Expression Data
    Associated Tools

    JBrowse - Visual display of RNA-Seq signals

    View Dmel\mir-10 in JBrowse
    RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
    Bulk Downloads
    RNA-Seq RPKM values for all genes
    Reference
    See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
    Developmental Proteome: Life Cycle
    Developmental Proteome: Embryogenesis
    External Data and Images
    Linkouts
    DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
    EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
    FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
    Images
    FlyBase Wiki
    Image Based Resources
    Alleles, Insertions, Transgenic Constructs, and Aberrations
    Classical and Insertion Alleles ( 1 )
    For All Classical and Insertion Alleles Show
     
    Other relevant insertions
    Transgenic Constructs ( 10 )
    For All Alleles Carried on Transgenic Constructs Show
    Transgenic constructs containing/affecting coding region of mir-10
    Transgenic constructs containing regulatory region of mir-10
    Aberrations (Deficiencies and Duplications) ( 0 )
    Inferred from experimentation ( 0 )
    Inferred from location ( 0 )
    Variants
    Variant Molecular Consequences
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    Orthologs
    Downloads
    Download All DIOPT Orthologs
    Human Orthologs (via DIOPT v9.1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    Domainoid
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Complementation?
    Transgene?
    Homo sapiens (Human) (3)
    Hsap\MIR10A
    1 of 14
    Yes
    Yes
    Hsap\MIR10B
    1 of 14
    Yes
    Yes
    Hsap\MIR99A
    1 of 14
    Yes
    Yes
    Model Organism Orthologs (via DIOPT v9.1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    Domainoid
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    SonicParanoid
    Alignment
    Complementation?
    Transgene?
    Rattus norvegicus (Norway rat) (3)
    Rnor\Mir10a
    1 of 14
    Yes
    Yes
    Rnor\Mir10b
    1 of 14
    Yes
    Yes
    Rnor\Mir99a
    1 of 14
    Yes
    Yes
    Mus musculus (laboratory mouse) (3)
    Mmus\Mir10a
    1 of 14
    Yes
    Yes
    Mmus\Mir10b
    1 of 14
    Yes
    Yes
    Mmus\Mir99a
    1 of 14
    Yes
    Yes
    Xenopus tropicalis (Western clawed frog) (0)
    Danio rerio (Zebrafish) (7)
    Drer\mir10a
    1 of 14
    Yes
    Yes
    Drer\mir10b-1
    1 of 14
    Yes
    Yes
    Drer\mir10b-2
    1 of 14
    Yes
    Yes
    Drer\mir10c
    1 of 14
    Yes
    Yes
    Drer\mir10d
    1 of 14
    Yes
    Yes
    Drer\mir99-1
    1 of 14
    Yes
    Yes
    Drer\mir99-2
    1 of 14
    Yes
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (0)
    Anopheles gambiae (African malaria mosquito) (0)
    Arabidopsis thaliana (thale-cress) (0)
    Saccharomyces cerevisiae (Brewer's yeast) (0)
    Schizosaccharomyces pombe (Fission yeast) (0)
    Escherichia coli (enterobacterium) (0)
    Other Organism Orthologs (via OrthoDB)
    Data provided directly from OrthoDB:mir-10. Refer to their site for version information.
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v9.1)
    Human Disease Associations
    FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    Please see the Physical Interaction reports below for full details
    RNA-protein
    Physical Interaction
    Assay
    References
    mir-10 - AGO1
    anti bait coimmunoprecipitation, northern blot
    (Lim et al., 2020, Okamura et al., 2008)
    Summary of Genetic Interactions
    esyN Network Diagram
    Other Interaction Browsers
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    Pathways
    Signaling Pathways (FlyBase)
    Negative Regulators of Hedgehog Signaling Pathway -
    Negative regulators of hedgehog signaling down-regulate the pathway, resulting in the repression of transcription of hh-responsive genes.
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-48
    Cytogenetic map
    84A5-84A5
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    84A5-84A5
    Limits computationally determined from genome sequence between P{PZ}pb04498 and P{lacW}l(3)L2100L2100
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-48

    (FlyBase, 2016)

    3-44.2

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (37)
    cDNA Clones (0)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
      Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

          cDNA Clones, End Sequenced (ESTs)
          BDGP DGC clones
            Other clones
              RNAi and Array Information
              Linkouts
              Antibody Information
              Laboratory Generated Antibodies
               
              Commercially Available Antibodies
               
              Cell Line Information
              Publicly Available Cell Lines
               
                Other Stable Cell Lines
                 
                  Other Comments

                  New annotation (CR33565) in release 4.1 of the genome annotation.

                  (FlyBase Genome Annotators, 2005)

                  New annotation (CR32942) in release 3 of the genome annotation.

                  (FlyBase Genome Annotators, 2002-2003)
                  Relationship to Other Genes
                  Source for database merge of

                  Source for merge of: mir-10 mir-10S

                  (FlyBase Genome Annotators, 2010)
                  Additional comments

                  The annotation for mir-10 has been changed in release 5.31 of the genome annotation, so that instead of representing a mature miRNA it now represents the precursor stem loop pre-miRNA. Thus the separate annotations (CR32942 and CR33565) which previously each represented one of the two mature miRNAs made from the mir-10 stem loop precursor have been converted into a single annotation (CR42977).

                  (FlyBase Genome Annotators, 2010)
                  Nomenclature History
                  Source for database identify of
                  Nomenclature comments
                  Etymology
                  Synonyms and Secondary IDs (17)
                  Reported As
                  Symbol Synonym
                  CR32942
                  (Ni et al., 2011.7.19)
                  CR33565
                  (FlyBase Genome Annotators, 2005)
                  CR42977
                  (FlyBase Genome Annotators, 2010)
                  MIR-10
                  (Ylla et al., 2016, Miura et al., 2011)
                  dme-miR-10
                  (Volin et al., 2018, Towler et al., 2015, Esslinger et al., 2013)
                  dme-miR-10-5p
                  (Chandra et al., 2015)
                  dme-mir-10
                  (He et al., 2022, miRBase, 2013, Huang and Gu, 2007)
                  miR-10
                  (Ramesh et al., 2023, Yang et al., 2023, Batut et al., 2022, Klann et al., 2021, Kitatani et al., 2020, Li et al., 2020, Lim et al., 2020, Richardson and Portela, 2018, Picao-Osorio et al., 2017, Shu et al., 2017, Wang et al., 2016, Fulga et al., 2015, Suh et al., 2015, Fu et al., 2014, Gummalla et al., 2014, Xia and Zhang, 2014, Mezan et al., 2013, Bejarano et al., 2012, Liu et al., 2012, Griffiths-Jones et al., 2011, Liu et al., 2011, Gehrke et al., 2010, Ghildiyal et al., 2010, Ibáñez-Ventoso et al., 2008, Lemons and McGinnis, 2008, Paré et al., 2008, Behura, 2007, Stark et al., 2007, Lemons and McGinnis, 2006, Leaman, 2005, Lemons and McGinnis, 2005, Sokol and Ambros, 2005, Stark et al., 2005, Kosman et al., 2004, Nakahara and Carthew, 2004, Enright et al., 2003, Lai et al., 2003, Schwarz et al., 2003, Sempere et al., 2003, Stark et al., 2003, Stark et al., 2003, Lagos-Quintana et al., 2001, Lee et al., 2001)
                  miR-10*
                  (Nesler et al., 2013, Stark et al., 2007)
                  miR-10-3p
                  (Fast et al., 2017)
                  miR-10-5p
                  (Hotzy et al., 2022)
                  miR-10a
                  (Orom et al., 2006)
                  mir-10
                  (Brener et al., 2023, Örkenby et al., 2023, Zsindely et al., 2023, Hanyu-Nakamura et al., 2019, Niu et al., 2019, Zhao et al., 2018, Mohammed and Lai, 2016.2.8, Javeed et al., 2015, Chen et al., 2014, Wang et al., 2014, Yeh et al., 2014, Daneshvar et al., 2013, Bejarano et al., 2012, Bejarano et al., 2012, Lemons et al., 2012, Schertel et al., 2012, Szuplewski et al., 2012, Qian et al., 2011, FlyBase Genome Annotators, 2010, Martin et al., 2009, Neumuller et al., 2008, Okamura et al., 2008, Ruby et al., 2007, Stark et al., 2007, Pearson et al., 2005)
                  mir-10*
                  (Aravin et al., 2003)
                  mir-10S
                  pri-mir-10
                  (Lemons et al., 2012)
                  Name Synonyms
                  mir-10
                  mir-10 stem loop
                  mir-10S
                  Secondary FlyBase IDs
                  • FBgn0046833
                  • FBgn0082182
                  • FBgn0262270
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  Study result (0)
                  Result
                  Result Type
                  Title
                  External Crossreferences and Linkouts ( 16 )
                  Sequence Crossreferences
                  NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
                  GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
                  RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
                  RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms
                  Other crossreferences
                  DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                  EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                  FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                  KEGG Genes - Molecular building blocks of life in the genomic space.
                  MARRVEL_MODEL - MARRVEL (model organism gene)
                  miRBase - A searchable database of published miRNA sequences and annotation.
                  Linkouts
                  DroID - A comprehensive database of gene and protein interactions.
                  FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                  References (99)